Figure5A

Load Data

dataset <- read.delim("raw_data/Figure5A.txt", stringsAsFactors = FALSE)

dataset$genotype <- gsub(" ", "", dataset$genotype )
dataset$genotype <- factor(dataset$genotype)
dataset$Experiment <- factor(rep(paste0("exp", 1:(length(dataset$genotype)/length(levels(dataset$genotype)))), each=length(unique(dataset$genotype))))

dataset$siRNA <-  factor(gsub(".*[T,O]\\+","",dataset$genotype))
dataset$genotype <-  factor(gsub("\\+.*","",dataset$genotype))

dataset$UID <- factor(paste(dataset$Experiment, dataset$genotype, dataset$siRNA))
dataset$GSID <- factor(paste(dataset$genotype, dataset$siRNA))

# wide format
kable(dataset, row.names = F)

genotype	NT	olaparib_30nM	olaparib_300nM	olaparib_3000nM	Experiment	siRNA	UID	GSID
WT	2668	2328	2108	1012	exp1	siCtrl	exp1 WT siCtrl	WT siCtrl
WT	2336	1888	1336	796	exp1	si53BP1	exp1 WT si53BP1	WT si53BP1
WT	1080	804	486	246	exp1	siBRCA1	exp1 WT siBRCA1	WT siBRCA1
WT	1360	992	840	468	exp1	si53BP1+siBRCA1	exp1 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1
ALC1KO	1960	1040	576	378	exp1	siCtrl	exp1 ALC1KO siCtrl	ALC1KO siCtrl
ALC1KO	1672	792	536	388	exp1	si53BP1	exp1 ALC1KO si53BP1	ALC1KO si53BP1
ALC1KO	752	324	164	71	exp1	siBRCA1	exp1 ALC1KO siBRCA1	ALC1KO siBRCA1
ALC1KO	788	478	293	142	exp1	si53BP1+siBRCA1	exp1 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1
WT	3072	2864	2768	2084	exp2	siCtrl	exp2 WT siCtrl	WT siCtrl
WT	3208	2984	2500	1886	exp2	si53BP1	exp2 WT si53BP1	WT si53BP1
WT	2376	1352	1112	1020	exp2	siBRCA1	exp2 WT siBRCA1	WT siBRCA1
WT	2744	2592	2016	1832	exp2	si53BP1+siBRCA1	exp2 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1
ALC1KO	2064	1032	488	411	exp2	siCtrl	exp2 ALC1KO siCtrl	ALC1KO siCtrl
ALC1KO	1424	988	536	416	exp2	si53BP1	exp2 ALC1KO si53BP1	ALC1KO si53BP1
ALC1KO	372	195	94	68	exp2	siBRCA1	exp2 ALC1KO siBRCA1	ALC1KO siBRCA1
ALC1KO	612	153	64	45	exp2	si53BP1+siBRCA1	exp2 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1
WT	2744	2728	2464	1838	exp3	siCtrl	exp3 WT siCtrl	WT siCtrl
WT	2800	2608	2320	1748	exp3	si53BP1	exp3 WT si53BP1	WT si53BP1
WT	1848	1256	1020	768	exp3	siBRCA1	exp3 WT siBRCA1	WT siBRCA1
WT	2328	2624	2104	2064	exp3	si53BP1+siBRCA1	exp3 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1
ALC1KO	2048	988	812	540	exp3	siCtrl	exp3 ALC1KO siCtrl	ALC1KO siCtrl
ALC1KO	1624	1096	528	304	exp3	si53BP1	exp3 ALC1KO si53BP1	ALC1KO si53BP1
ALC1KO	380	376	126	47	exp3	siBRCA1	exp3 ALC1KO siBRCA1	ALC1KO siBRCA1
ALC1KO	896	288	168	75	exp3	si53BP1+siBRCA1	exp3 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1
WT	1576	1496	1328	948	exp4	siCtrl	exp4 WT siCtrl	WT siCtrl
WT	2088	1960	1856	1076	exp4	si53BP1	exp4 WT si53BP1	WT si53BP1
WT	608	512	376	191	exp4	siBRCA1	exp4 WT siBRCA1	WT siBRCA1
WT	1352	960	796	876	exp4	si53BP1+siBRCA1	exp4 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1
ALC1KO	1304	436	396	85	exp4	siCtrl	exp4 ALC1KO siCtrl	ALC1KO siCtrl
ALC1KO	370	184	111	38	exp4	si53BP1	exp4 ALC1KO si53BP1	ALC1KO si53BP1
ALC1KO	580	224	108	11	exp4	siBRCA1	exp4 ALC1KO siBRCA1	ALC1KO siBRCA1
ALC1KO	1416	712	500	312	exp4	si53BP1+siBRCA1	exp4 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1

library(reshape2)
# reshape to long format
dataset <- melt(dataset, variable.name = "Treatment", value.name = "Counts")

dataset$genotype <- relevel(dataset$genotype, ref = "WT")
dataset$siRNA <- relevel(dataset$siRNA, ref = "siCtrl")
dataset$UID <- relevel(dataset$UID, ref = "exp1 WT siCtrl")

dataset$Olaparib <- gsub("NT","1",dataset$Treatment)
dataset$Olaparib <- gsub("olaparib_|nM","",dataset$Olaparib)
dataset$Olaparib <- log10(as.integer(dataset$Olaparib))




dataset$Offset <- NA
for(uid in levels(dataset$UID)){
        dataset$Offset[dataset$UID == uid] <- mean(dataset$Counts[dataset$UID == uid])
}

dataset$NormCounts <- dataset$Counts / dataset$Offset



dataset$Offset2 <- NA
for(gsid in levels(dataset$GSID)){
        dataset$Offset2[dataset$GSID == gsid] <- mean(dataset$NormCounts[dataset$GSID == gsid & dataset$Olaparib == 0])
}

dataset$NormCounts2 <- dataset$NormCounts / dataset$Offset2



# long format
kable(dataset, row.names = F)

genotype	Experiment	siRNA	UID	GSID	Treatment	Counts	Olaparib	Offset	NormCounts	Offset2	NormCounts2
WT	exp1	siCtrl	exp1 WT siCtrl	WT siCtrl	NT	2668	0.000000	2029.00	1.3149335	1.188929	1.1059818
WT	exp1	si53BP1	exp1 WT si53BP1	WT si53BP1	NT	2336	0.000000	1589.00	1.4701070	1.265421	1.1617529
WT	exp1	siBRCA1	exp1 WT siBRCA1	WT siBRCA1	NT	1080	0.000000	654.00	1.6513761	1.556467	1.0609770
WT	exp1	si53BP1+siBRCA1	exp1 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	NT	1360	0.000000	915.00	1.4863388	1.264986	1.1749846
ALC1KO	exp1	siCtrl	exp1 ALC1KO siCtrl	ALC1KO siCtrl	NT	1960	0.000000	988.50	1.9828022	2.066197	0.9596386
ALC1KO	exp1	si53BP1	exp1 ALC1KO si53BP1	ALC1KO si53BP1	NT	1672	0.000000	847.00	1.9740260	1.900335	1.0387778
ALC1KO	exp1	siBRCA1	exp1 ALC1KO siBRCA1	ALC1KO siBRCA1	NT	752	0.000000	327.75	2.2944317	2.121324	1.0816038
ALC1KO	exp1	si53BP1+siBRCA1	exp1 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	NT	788	0.000000	425.25	1.8530276	2.273009	0.8152311
WT	exp2	siCtrl	exp2 WT siCtrl	WT siCtrl	NT	3072	0.000000	2697.00	1.1390434	1.188929	0.9580418
WT	exp2	si53BP1	exp2 WT si53BP1	WT si53BP1	NT	3208	0.000000	2644.50	1.2130838	1.265421	0.9586401
WT	exp2	siBRCA1	exp2 WT siBRCA1	WT siBRCA1	NT	2376	0.000000	1465.00	1.6218430	1.556467	1.0420025
WT	exp2	si53BP1+siBRCA1	exp2 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	NT	2744	0.000000	2296.00	1.1951220	1.264986	0.9447711
ALC1KO	exp2	siCtrl	exp2 ALC1KO siCtrl	ALC1KO siCtrl	NT	2064	0.000000	998.75	2.0665832	2.066197	1.0001871
ALC1KO	exp2	si53BP1	exp2 ALC1KO si53BP1	ALC1KO si53BP1	NT	1424	0.000000	841.00	1.6932224	1.900335	0.8910125
ALC1KO	exp2	siBRCA1	exp2 ALC1KO siBRCA1	ALC1KO siBRCA1	NT	372	0.000000	182.25	2.0411523	2.121324	0.9622069
ALC1KO	exp2	si53BP1+siBRCA1	exp2 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	NT	612	0.000000	218.50	2.8009153	2.273009	1.2322500
WT	exp3	siCtrl	exp3 WT siCtrl	WT siCtrl	NT	2744	0.000000	2443.50	1.1229793	1.188929	0.9445305
WT	exp3	si53BP1	exp3 WT si53BP1	WT si53BP1	NT	2800	0.000000	2369.00	1.1819333	1.265421	0.9340235
WT	exp3	siBRCA1	exp3 WT siBRCA1	WT siBRCA1	NT	1848	0.000000	1223.00	1.5110384	1.556467	0.9708127
WT	exp3	si53BP1+siBRCA1	exp3 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	NT	2328	0.000000	2280.00	1.0210526	1.264986	0.8071653
ALC1KO	exp3	siCtrl	exp3 ALC1KO siCtrl	ALC1KO siCtrl	NT	2048	0.000000	1097.00	1.8669098	2.066197	0.9035489
ALC1KO	exp3	si53BP1	exp3 ALC1KO si53BP1	ALC1KO si53BP1	NT	1624	0.000000	888.00	1.8288288	1.900335	0.9623718
ALC1KO	exp3	siBRCA1	exp3 ALC1KO siBRCA1	ALC1KO siBRCA1	NT	380	0.000000	232.25	1.6361679	2.121324	0.7712957
ALC1KO	exp3	si53BP1+siBRCA1	exp3 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	NT	896	0.000000	356.75	2.5115627	2.273009	1.1049506
WT	exp4	siCtrl	exp4 WT siCtrl	WT siCtrl	NT	1576	0.000000	1337.00	1.1787584	1.188929	0.9914459
WT	exp4	si53BP1	exp4 WT si53BP1	WT si53BP1	NT	2088	0.000000	1745.00	1.1965616	1.265421	0.9455835
WT	exp4	siBRCA1	exp4 WT siBRCA1	WT siBRCA1	NT	608	0.000000	421.75	1.4416123	1.556467	0.9262078
WT	exp4	si53BP1+siBRCA1	exp4 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	NT	1352	0.000000	996.00	1.3574297	1.264986	1.0730790
ALC1KO	exp4	siCtrl	exp4 ALC1KO siCtrl	ALC1KO siCtrl	NT	1304	0.000000	555.25	2.3484917	2.066197	1.1366254
ALC1KO	exp4	si53BP1	exp4 ALC1KO si53BP1	ALC1KO si53BP1	NT	370	0.000000	175.75	2.1052632	1.900335	1.1078379
ALC1KO	exp4	siBRCA1	exp4 ALC1KO siBRCA1	ALC1KO siBRCA1	NT	580	0.000000	230.75	2.5135428	2.121324	1.1848936
ALC1KO	exp4	si53BP1+siBRCA1	exp4 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	NT	1416	0.000000	735.00	1.9265306	2.273009	0.8475684
WT	exp1	siCtrl	exp1 WT siCtrl	WT siCtrl	olaparib_30nM	2328	1.477121	2029.00	1.1473632	1.188929	0.9650396
WT	exp1	si53BP1	exp1 WT si53BP1	WT si53BP1	olaparib_30nM	1888	1.477121	1589.00	1.1881687	1.265421	0.9389510
WT	exp1	siBRCA1	exp1 WT siBRCA1	WT siBRCA1	olaparib_30nM	804	1.477121	654.00	1.2293578	1.556467	0.7898384
WT	exp1	si53BP1+siBRCA1	exp1 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	olaparib_30nM	992	1.477121	915.00	1.0841530	1.264986	0.8570476
ALC1KO	exp1	siCtrl	exp1 ALC1KO siCtrl	ALC1KO siCtrl	olaparib_30nM	1040	1.477121	988.50	1.0520991	2.066197	0.5091960
ALC1KO	exp1	si53BP1	exp1 ALC1KO si53BP1	ALC1KO si53BP1	olaparib_30nM	792	1.477121	847.00	0.9350649	1.900335	0.4920527
ALC1KO	exp1	siBRCA1	exp1 ALC1KO siBRCA1	ALC1KO siBRCA1	olaparib_30nM	324	1.477121	327.75	0.9885584	2.121324	0.4660101
ALC1KO	exp1	si53BP1+siBRCA1	exp1 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	olaparib_30nM	478	1.477121	425.25	1.1240447	2.273009	0.4945183
WT	exp2	siCtrl	exp2 WT siCtrl	WT siCtrl	olaparib_30nM	2864	1.477121	2697.00	1.0619207	1.188929	0.8931744
WT	exp2	si53BP1	exp2 WT si53BP1	WT si53BP1	olaparib_30nM	2984	1.477121	2644.50	1.1283797	1.265421	0.8917027
WT	exp2	siBRCA1	exp2 WT siBRCA1	WT siBRCA1	olaparib_30nM	1352	1.477121	1465.00	0.9228669	1.556467	0.5929240
WT	exp2	si53BP1+siBRCA1	exp2 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	olaparib_30nM	2592	1.477121	2296.00	1.1289199	1.264986	0.8924368
ALC1KO	exp2	siCtrl	exp2 ALC1KO siCtrl	ALC1KO siCtrl	olaparib_30nM	1032	1.477121	998.75	1.0332916	2.066197	0.5000935
ALC1KO	exp2	si53BP1	exp2 ALC1KO si53BP1	ALC1KO si53BP1	olaparib_30nM	988	1.477121	841.00	1.1747919	1.900335	0.6182025
ALC1KO	exp2	siBRCA1	exp2 ALC1KO siBRCA1	ALC1KO siBRCA1	olaparib_30nM	195	1.477121	182.25	1.0699588	2.121324	0.5043826
ALC1KO	exp2	si53BP1+siBRCA1	exp2 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	olaparib_30nM	153	1.477121	218.50	0.7002288	2.273009	0.3080625
WT	exp3	siCtrl	exp3 WT siCtrl	WT siCtrl	olaparib_30nM	2728	1.477121	2443.50	1.1164313	1.188929	0.9390230
WT	exp3	si53BP1	exp3 WT si53BP1	WT si53BP1	olaparib_30nM	2608	1.477121	2369.00	1.1008864	1.265421	0.8699762
WT	exp3	siBRCA1	exp3 WT siBRCA1	WT siBRCA1	olaparib_30nM	1256	1.477121	1223.00	1.0269828	1.556467	0.6598164
WT	exp3	si53BP1+siBRCA1	exp3 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	olaparib_30nM	2624	1.477121	2280.00	1.1508772	1.264986	0.9097946
ALC1KO	exp3	siCtrl	exp3 ALC1KO siCtrl	ALC1KO siCtrl	olaparib_30nM	988	1.477121	1097.00	0.9006381	2.066197	0.4358917
ALC1KO	exp3	si53BP1	exp3 ALC1KO si53BP1	ALC1KO si53BP1	olaparib_30nM	1096	1.477121	888.00	1.2342342	1.900335	0.6494824
ALC1KO	exp3	siBRCA1	exp3 ALC1KO siBRCA1	ALC1KO siBRCA1	olaparib_30nM	376	1.477121	232.25	1.6189451	2.121324	0.7631768
ALC1KO	exp3	si53BP1+siBRCA1	exp3 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	olaparib_30nM	288	1.477121	356.75	0.8072880	2.273009	0.3551627
WT	exp4	siCtrl	exp4 WT siCtrl	WT siCtrl	olaparib_30nM	1496	1.477121	1337.00	1.1189230	1.188929	0.9411187
WT	exp4	si53BP1	exp4 WT si53BP1	WT si53BP1	olaparib_30nM	1960	1.477121	1745.00	1.1232092	1.265421	0.8876167
WT	exp4	siBRCA1	exp4 WT siBRCA1	WT siBRCA1	olaparib_30nM	512	1.477121	421.75	1.2139893	1.556467	0.7799645
WT	exp4	si53BP1+siBRCA1	exp4 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	olaparib_30nM	960	1.477121	996.00	0.9638554	1.264986	0.7619496
ALC1KO	exp4	siCtrl	exp4 ALC1KO siCtrl	ALC1KO siCtrl	olaparib_30nM	436	1.477121	555.25	0.7852319	2.066197	0.3800373
ALC1KO	exp4	si53BP1	exp4 ALC1KO si53BP1	ALC1KO si53BP1	olaparib_30nM	184	1.477121	175.75	1.0469417	1.900335	0.5509248
ALC1KO	exp4	siBRCA1	exp4 ALC1KO siBRCA1	ALC1KO siBRCA1	olaparib_30nM	224	1.477121	230.75	0.9707476	2.121324	0.4576141
ALC1KO	exp4	si53BP1+siBRCA1	exp4 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	olaparib_30nM	712	1.477121	735.00	0.9687075	2.273009	0.4261784
WT	exp1	siCtrl	exp1 WT siCtrl	WT siCtrl	olaparib_300nM	2108	2.477121	2029.00	1.0389354	1.188929	0.8738417
WT	exp1	si53BP1	exp1 WT si53BP1	WT si53BP1	olaparib_300nM	1336	2.477121	1589.00	0.8407804	1.265421	0.6644272
WT	exp1	siBRCA1	exp1 WT siBRCA1	WT siBRCA1	olaparib_300nM	486	2.477121	654.00	0.7431193	1.556467	0.4774396
WT	exp1	si53BP1+siBRCA1	exp1 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	olaparib_300nM	840	2.477121	915.00	0.9180328	1.264986	0.7257258
ALC1KO	exp1	siCtrl	exp1 ALC1KO siCtrl	ALC1KO siCtrl	olaparib_300nM	576	2.477121	988.50	0.5827011	2.066197	0.2820163
ALC1KO	exp1	si53BP1	exp1 ALC1KO si53BP1	ALC1KO si53BP1	olaparib_300nM	536	2.477121	847.00	0.6328217	1.900335	0.3330053
ALC1KO	exp1	siBRCA1	exp1 ALC1KO siBRCA1	ALC1KO siBRCA1	olaparib_300nM	164	2.477121	327.75	0.5003814	2.121324	0.2358817
ALC1KO	exp1	si53BP1+siBRCA1	exp1 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	olaparib_300nM	293	2.477121	425.25	0.6890065	2.273009	0.3031253
WT	exp2	siCtrl	exp2 WT siCtrl	WT siCtrl	olaparib_300nM	2768	2.477121	2697.00	1.0263255	1.188929	0.8632356
WT	exp2	si53BP1	exp2 WT si53BP1	WT si53BP1	olaparib_300nM	2500	2.477121	2644.50	0.9453583	1.265421	0.7470699
WT	exp2	siBRCA1	exp2 WT siBRCA1	WT siBRCA1	olaparib_300nM	1112	2.477121	1465.00	0.7590444	1.556467	0.4876712
WT	exp2	si53BP1+siBRCA1	exp2 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	olaparib_300nM	2016	2.477121	2296.00	0.8780488	1.264986	0.6941175
ALC1KO	exp2	siCtrl	exp2 ALC1KO siCtrl	ALC1KO siCtrl	olaparib_300nM	488	2.477121	998.75	0.4886108	2.066197	0.2364783
ALC1KO	exp2	si53BP1	exp2 ALC1KO si53BP1	ALC1KO si53BP1	olaparib_300nM	536	2.477121	841.00	0.6373365	1.900335	0.3353811
ALC1KO	exp2	siBRCA1	exp2 ALC1KO siBRCA1	ALC1KO siBRCA1	olaparib_300nM	94	2.477121	182.25	0.5157750	2.121324	0.2431383
ALC1KO	exp2	si53BP1+siBRCA1	exp2 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	olaparib_300nM	64	2.477121	218.50	0.2929062	2.273009	0.1288627
WT	exp3	siCtrl	exp3 WT siCtrl	WT siCtrl	olaparib_300nM	2464	2.477121	2443.50	1.0083896	1.188929	0.8481498
WT	exp3	si53BP1	exp3 WT si53BP1	WT si53BP1	olaparib_300nM	2320	2.477121	2369.00	0.9793162	1.265421	0.7739052
WT	exp3	siBRCA1	exp3 WT siBRCA1	WT siBRCA1	olaparib_300nM	1020	2.477121	1223.00	0.8340147	1.556467	0.5358382
WT	exp3	si53BP1+siBRCA1	exp3 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	olaparib_300nM	2104	2.477121	2280.00	0.9228070	1.264986	0.7294999
ALC1KO	exp3	siCtrl	exp3 ALC1KO siCtrl	ALC1KO siCtrl	olaparib_300nM	812	2.477121	1097.00	0.7402005	2.066197	0.3582430
ALC1KO	exp3	si53BP1	exp3 ALC1KO si53BP1	ALC1KO si53BP1	olaparib_300nM	528	2.477121	888.00	0.5945946	1.900335	0.3128893
ALC1KO	exp3	siBRCA1	exp3 ALC1KO siBRCA1	ALC1KO siBRCA1	olaparib_300nM	126	2.477121	232.25	0.5425188	2.121324	0.2557454
ALC1KO	exp3	si53BP1+siBRCA1	exp3 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	olaparib_300nM	168	2.477121	356.75	0.4709180	2.273009	0.2071782
WT	exp4	siCtrl	exp4 WT siCtrl	WT siCtrl	olaparib_300nM	1328	2.477121	1337.00	0.9932685	1.188929	0.8354316
WT	exp4	si53BP1	exp4 WT si53BP1	WT si53BP1	olaparib_300nM	1856	2.477121	1745.00	1.0636103	1.265421	0.8405187
WT	exp4	siBRCA1	exp4 WT siBRCA1	WT siBRCA1	olaparib_300nM	376	2.477121	421.75	0.8915234	1.556467	0.5727864
WT	exp4	si53BP1+siBRCA1	exp4 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	olaparib_300nM	796	2.477121	996.00	0.7991968	1.264986	0.6317832
ALC1KO	exp4	siCtrl	exp4 ALC1KO siCtrl	ALC1KO siCtrl	olaparib_300nM	396	2.477121	555.25	0.7131923	2.066197	0.3451715
ALC1KO	exp4	si53BP1	exp4 ALC1KO si53BP1	ALC1KO si53BP1	olaparib_300nM	111	2.477121	175.75	0.6315789	1.900335	0.3323514
ALC1KO	exp4	siBRCA1	exp4 ALC1KO siBRCA1	ALC1KO siBRCA1	olaparib_300nM	108	2.477121	230.75	0.4680390	2.121324	0.2206354
ALC1KO	exp4	si53BP1+siBRCA1	exp4 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	olaparib_300nM	500	2.477121	735.00	0.6802721	2.273009	0.2992826
WT	exp1	siCtrl	exp1 WT siCtrl	WT siCtrl	olaparib_3000nM	1012	3.477121	2029.00	0.4987679	1.188929	0.4195103
WT	exp1	si53BP1	exp1 WT si53BP1	WT si53BP1	olaparib_3000nM	796	3.477121	1589.00	0.5009440	1.265421	0.3958713
WT	exp1	siBRCA1	exp1 WT siBRCA1	WT siBRCA1	olaparib_3000nM	246	3.477121	654.00	0.3761468	1.556467	0.2416670
WT	exp1	si53BP1+siBRCA1	exp1 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	olaparib_3000nM	468	3.477121	915.00	0.5114754	1.264986	0.4043329
ALC1KO	exp1	siCtrl	exp1 ALC1KO siCtrl	ALC1KO siCtrl	olaparib_3000nM	378	3.477121	988.50	0.3823976	2.066197	0.1850732
ALC1KO	exp1	si53BP1	exp1 ALC1KO si53BP1	ALC1KO si53BP1	olaparib_3000nM	388	3.477121	847.00	0.4580874	1.900335	0.2410561
ALC1KO	exp1	siBRCA1	exp1 ALC1KO siBRCA1	ALC1KO siBRCA1	olaparib_3000nM	71	3.477121	327.75	0.2166285	2.121324	0.1021195
ALC1KO	exp1	si53BP1+siBRCA1	exp1 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	olaparib_3000nM	142	3.477121	425.25	0.3339212	2.273009	0.1469071
WT	exp2	siCtrl	exp2 WT siCtrl	WT siCtrl	olaparib_3000nM	2084	3.477121	2697.00	0.7727104	1.188929	0.6499216
WT	exp2	si53BP1	exp2 WT si53BP1	WT si53BP1	olaparib_3000nM	1886	3.477121	2644.50	0.7131783	1.265421	0.5635896
WT	exp2	siBRCA1	exp2 WT siBRCA1	WT siBRCA1	olaparib_3000nM	1020	3.477121	1465.00	0.6962457	1.556467	0.4473243
WT	exp2	si53BP1+siBRCA1	exp2 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	olaparib_3000nM	1832	3.477121	2296.00	0.7979094	1.264986	0.6307655
ALC1KO	exp2	siCtrl	exp2 ALC1KO siCtrl	ALC1KO siCtrl	olaparib_3000nM	411	3.477121	998.75	0.4115144	2.066197	0.1991652
ALC1KO	exp2	si53BP1	exp2 ALC1KO si53BP1	ALC1KO si53BP1	olaparib_3000nM	416	3.477121	841.00	0.4946492	1.900335	0.2602958
ALC1KO	exp2	siBRCA1	exp2 ALC1KO siBRCA1	ALC1KO siBRCA1	olaparib_3000nM	68	3.477121	182.25	0.3731139	2.121324	0.1758873
ALC1KO	exp2	si53BP1+siBRCA1	exp2 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	olaparib_3000nM	45	3.477121	218.50	0.2059497	2.273009	0.0906066
WT	exp3	siCtrl	exp3 WT siCtrl	WT siCtrl	olaparib_3000nM	1838	3.477121	2443.50	0.7521997	1.188929	0.6326702
WT	exp3	si53BP1	exp3 WT si53BP1	WT si53BP1	olaparib_3000nM	1748	3.477121	2369.00	0.7378641	1.265421	0.5830975
WT	exp3	siBRCA1	exp3 WT siBRCA1	WT siBRCA1	olaparib_3000nM	768	3.477121	1223.00	0.6279640	1.556467	0.4034546
WT	exp3	si53BP1+siBRCA1	exp3 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	olaparib_3000nM	2064	3.477121	2280.00	0.9052632	1.264986	0.7156311
ALC1KO	exp3	siCtrl	exp3 ALC1KO siCtrl	ALC1KO siCtrl	olaparib_3000nM	540	3.477121	1097.00	0.4922516	2.066197	0.2382404
ALC1KO	exp3	si53BP1	exp3 ALC1KO si53BP1	ALC1KO si53BP1	olaparib_3000nM	304	3.477121	888.00	0.3423423	1.900335	0.1801484
ALC1KO	exp3	siBRCA1	exp3 ALC1KO siBRCA1	ALC1KO siBRCA1	olaparib_3000nM	47	3.477121	232.25	0.2023681	2.121324	0.0953971
ALC1KO	exp3	si53BP1+siBRCA1	exp3 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	olaparib_3000nM	75	3.477121	356.75	0.2102313	2.273009	0.0924903
WT	exp4	siCtrl	exp4 WT siCtrl	WT siCtrl	olaparib_3000nM	948	3.477121	1337.00	0.7090501	1.188929	0.5963773
WT	exp4	si53BP1	exp4 WT si53BP1	WT si53BP1	olaparib_3000nM	1076	3.477121	1745.00	0.6166189	1.265421	0.4872834
WT	exp4	siBRCA1	exp4 WT siBRCA1	WT siBRCA1	olaparib_3000nM	191	3.477121	421.75	0.4528749	1.556467	0.2909633
WT	exp4	si53BP1+siBRCA1	exp4 WT si53BP1+siBRCA1	WT si53BP1+siBRCA1	olaparib_3000nM	876	3.477121	996.00	0.8795181	1.264986	0.6952790
ALC1KO	exp4	siCtrl	exp4 ALC1KO siCtrl	ALC1KO siCtrl	olaparib_3000nM	85	3.477121	555.25	0.1530842	2.066197	0.0740898
ALC1KO	exp4	si53BP1	exp4 ALC1KO si53BP1	ALC1KO si53BP1	olaparib_3000nM	38	3.477121	175.75	0.2162162	1.900335	0.1137779
ALC1KO	exp4	siBRCA1	exp4 ALC1KO siBRCA1	ALC1KO siBRCA1	olaparib_3000nM	11	3.477121	230.75	0.0476706	2.121324	0.0224721
ALC1KO	exp4	si53BP1+siBRCA1	exp4 ALC1KO si53BP1+siBRCA1	ALC1KO si53BP1+siBRCA1	olaparib_3000nM	312	3.477121	735.00	0.4244898	2.273009	0.1867524

Plot Data

library(ggplot2)

# raw data
ggplot(dataset, aes(x=Olaparib, y=Counts)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_smooth(method=lm, formula = y ~ poly(x,2), se=FALSE, aes(colour=siRNA)) +
        geom_point(aes(colour=siRNA, shape=Experiment), size=2) +        
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)") +
        scale_shape_manual(values=15:19) +
        scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

# NormCounts Linear
ggplot(dataset, aes(x=Olaparib, y=NormCounts, color=siRNA)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_point(aes(colour=siRNA), size=2) +        
        geom_smooth(method=lm, formula = y ~ x, se=FALSE) +
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)") +
        scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

# NormCounts2 Linear
ggplot(dataset, aes(x=Olaparib, y=NormCounts2, color=siRNA)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_point(aes(colour=siRNA), size=2) +        
        geom_smooth(method=lm, formula = y ~ x, se=FALSE) +
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)") +
        scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

# NormCounts Quadratic
ggplot(dataset, aes(x=Olaparib, y=NormCounts, color=siRNA)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_point(aes(colour=siRNA), size=2) +        
        geom_smooth(method=lm, formula = y ~ poly(x,2), se=FALSE) +
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)")+
        scale_color_manual(values=c("#000000","#008000","#808080","#008080")) 

# NormCounts2 Quadratic
ggplot(dataset, aes(x=Olaparib, y=NormCounts2, color=siRNA)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_point(aes(colour=siRNA), size=2) +        
        geom_smooth(method=lm, formula = y ~ poly(x,2), se=FALSE) +
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)") +
        scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

# NormCounts Cubic
ggplot(dataset, aes(x=Olaparib, y=NormCounts, color=siRNA)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_point(aes(colour=siRNA), size=2) +        
        geom_smooth(method=lm, formula = y ~ poly(x,3), se=FALSE) +
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)")+
        scale_color_manual(values=c("#000000","#008000","#808080","#008080")) 

# NormCounts2 Cubic
ggplot(dataset, aes(x=Olaparib, y=NormCounts2, color=siRNA)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_point(aes(colour=siRNA), size=2) +        
        geom_smooth(method=lm, formula = y ~ poly(x,3), se=FALSE) +
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)") +
        scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

library(Cairo)

cairo_pdf("Figure5A.pdf", width = 8, height = 4, family = "Arial")

ggplot(dataset, aes(x=Olaparib, y=NormCounts2)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_point(aes(colour = siRNA)) +
        geom_smooth(method=lm, formula = y ~ poly(x,2), se=TRUE, aes(colour = siRNA), fill='#DDDDDD', size=0.5) +
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)") +
        ylab(label = "Normalized Counts") +
        scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

dev.off()

## quartz_off_screen 
##                 2

Models

library(MASS)
library(DHARMa)
library(lme4)
library(lmerTest)
library(bbmle)

Linear formula

fit1 <- lm(Counts ~ Experiment + Olaparib*siRNA*genotype, data = dataset)
print(summary(fit1))

## 
## Call:
## lm(formula = Counts ~ Experiment + Olaparib * siRNA * genotype, 
##     data = dataset)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -713.14 -258.88   18.63  224.08  920.16 
## 
## Coefficients:
##                                               Estimate Std. Error t value
## (Intercept)                                   2486.513    167.388  14.855
## Experimentexp2                                 445.938     89.908   4.960
## Experimentexp3                                 389.250     89.908   4.329
## Experimentexp4                                -197.375     89.908  -2.195
## Olaparib                                      -279.540     69.982  -3.994
## siRNAsi53BP1                                    80.926    223.550   0.362
## siRNAsi53BP1+siBRCA1                          -662.557    223.550  -2.964
## siRNAsiBRCA1                                 -1211.136    223.550  -5.418
## genotypeALC1KO                                -938.475    223.550  -4.198
## Olaparib:siRNAsi53BP1                          -64.955     98.969  -0.656
## Olaparib:siRNAsi53BP1+siBRCA1                   84.874     98.969   0.858
## Olaparib:siRNAsiBRCA1                           13.698     98.969   0.138
## Olaparib:genotypeALC1KO                       -149.784     98.969  -1.513
## siRNAsi53BP1:genotypeALC1KO                   -558.350    316.148  -1.766
## siRNAsi53BP1+siBRCA1:genotypeALC1KO           -192.261    316.148  -0.608
## siRNAsiBRCA1:genotypeALC1KO                      5.367    316.148   0.017
## Olaparib:siRNAsi53BP1:genotypeALC1KO           202.473    139.964   1.447
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO   119.029    139.964   0.850
## Olaparib:siRNAsiBRCA1:genotypeALC1KO           276.501    139.964   1.976
##                                              Pr(>|t|)    
## (Intercept)                                   < 2e-16 ***
## Experimentexp2                               2.61e-06 ***
## Experimentexp3                               3.33e-05 ***
## Experimentexp4                               0.030262 *  
## Olaparib                                     0.000118 ***
## siRNAsi53BP1                                 0.718051    
## siRNAsi53BP1+siBRCA1                         0.003732 ** 
## siRNAsiBRCA1                                 3.64e-07 ***
## genotypeALC1KO                               5.52e-05 ***
## Olaparib:siRNAsi53BP1                        0.513007    
## Olaparib:siRNAsi53BP1+siBRCA1                0.393008    
## Olaparib:siRNAsiBRCA1                        0.890178    
## Olaparib:genotypeALC1KO                      0.133063    
## siRNAsi53BP1:genotypeALC1KO                  0.080178 .  
## siRNAsi53BP1+siBRCA1:genotypeALC1KO          0.544362    
## siRNAsiBRCA1:genotypeALC1KO                  0.986486    
## Olaparib:siRNAsi53BP1:genotypeALC1KO         0.150876    
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.396954    
## Olaparib:siRNAsiBRCA1:genotypeALC1KO         0.050737 .  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 359.6 on 109 degrees of freedom
## Multiple R-squared:  0.8584, Adjusted R-squared:  0.835 
## F-statistic: 36.71 on 18 and 109 DF,  p-value: < 2.2e-16

cat("AIC: ", AIC(fit1))

## AIC:  1889.261

simres <- simulateResiduals(fittedModel = fit1)
plot(simres)

fit2 <- lm(NormCounts ~ Olaparib*siRNA*genotype, data = dataset)
print(summary(fit2))

## 
## Call:
## lm(formula = NormCounts ~ Olaparib * siRNA * genotype, data = dataset)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -0.5166 -0.1169  0.0066  0.1040  0.7429 
## 
## Coefficients:
##                                              Estimate Std. Error t value
## (Intercept)                                   1.25213    0.08809  14.215
## Olaparib                                     -0.13571    0.03900  -3.480
## siRNAsi53BP1                                  0.07162    0.12457   0.575
## siRNAsi53BP1+siBRCA1                          0.01937    0.12457   0.155
## siRNAsiBRCA1                                  0.29335    0.12457   2.355
## genotypeALC1KO                                0.65514    0.12457   5.259
## Olaparib:siRNAsi53BP1                        -0.03855    0.05515  -0.699
## Olaparib:siRNAsi53BP1+siBRCA1                -0.01043    0.05515  -0.189
## Olaparib:siRNAsiBRCA1                        -0.15790    0.05515  -2.863
## Olaparib:genotypeALC1KO                      -0.35263    0.05515  -6.394
## siRNAsi53BP1:genotypeALC1KO                  -0.14870    0.17617  -0.844
## siRNAsi53BP1+siBRCA1:genotypeALC1KO           0.13138    0.17617   0.746
## siRNAsiBRCA1:genotypeALC1KO                  -0.15105    0.17617  -0.857
## Olaparib:siRNAsi53BP1:genotypeALC1KO          0.08004    0.07799   1.026
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.07072    0.07799  -0.907
## Olaparib:siRNAsiBRCA1:genotypeALC1KO          0.08131    0.07799   1.042
##                                              Pr(>|t|)    
## (Intercept)                                   < 2e-16 ***
## Olaparib                                     0.000715 ***
## siRNAsi53BP1                                 0.566486    
## siRNAsi53BP1+siBRCA1                         0.876710    
## siRNAsiBRCA1                                 0.020270 *  
## genotypeALC1KO                               7.02e-07 ***
## Olaparib:siRNAsi53BP1                        0.485991    
## Olaparib:siRNAsi53BP1+siBRCA1                0.850393    
## Olaparib:siRNAsiBRCA1                        0.005009 ** 
## Olaparib:genotypeALC1KO                      3.84e-09 ***
## siRNAsi53BP1:genotypeALC1KO                  0.400415    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO          0.457374    
## siRNAsiBRCA1:genotypeALC1KO                  0.393037    
## Olaparib:siRNAsi53BP1:genotypeALC1KO         0.306980    
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.366510    
## Olaparib:siRNAsiBRCA1:genotypeALC1KO         0.299436    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.2004 on 112 degrees of freedom
## Multiple R-squared:  0.8791, Adjusted R-squared:  0.8629 
## F-statistic: 54.27 on 15 and 112 DF,  p-value: < 2.2e-16

cat("AIC: ", AIC(fit2))

## AIC:  -31.34769

simres <- simulateResiduals(fittedModel = fit2)
plot(simres)

fit3 <- lm(NormCounts2 ~ Olaparib*siRNA*genotype, data = dataset)
print(summary(fit3))

## 
## Call:
## lm(formula = NormCounts2 ~ Olaparib * siRNA * genotype, data = dataset)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -0.23675 -0.06789  0.00460  0.06796  0.32683 
## 
## Coefficients:
##                                               Estimate Std. Error t value
## (Intercept)                                   1.053158   0.047016  22.400
## Olaparib                                     -0.114146   0.020815  -5.484
## siRNAsi53BP1                                 -0.007063   0.066491  -0.106
## siRNAsi53BP1+siBRCA1                         -0.048008   0.066491  -0.722
## siRNAsiBRCA1                                 -0.060219   0.066491  -0.906
## genotypeALC1KO                               -0.130076   0.066491  -1.956
## Olaparib:siRNAsi53BP1                        -0.023565   0.029437  -0.801
## Olaparib:siRNAsi53BP1+siBRCA1                -0.001379   0.029437  -0.047
## Olaparib:siRNAsiBRCA1                        -0.074492   0.029437  -2.531
## Olaparib:genotypeALC1KO                      -0.122204   0.029437  -4.151
## siRNAsi53BP1:genotypeALC1KO                   0.047067   0.094032   0.501
## siRNAsi53BP1+siBRCA1:genotypeALC1KO           0.030343   0.094032   0.323
## siRNAsiBRCA1:genotypeALC1KO                   0.103308   0.094032   1.099
## Olaparib:siRNAsi53BP1:genotypeALC1KO          0.024770   0.041630   0.595
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.012815   0.041630  -0.308
## Olaparib:siRNAsiBRCA1:genotypeALC1KO          0.044529   0.041630   1.070
##                                              Pr(>|t|)    
## (Intercept)                                   < 2e-16 ***
## Olaparib                                     2.61e-07 ***
## siRNAsi53BP1                                   0.9156    
## siRNAsi53BP1+siBRCA1                           0.4718    
## siRNAsiBRCA1                                   0.3671    
## genotypeALC1KO                                 0.0529 .  
## Olaparib:siRNAsi53BP1                          0.4251    
## Olaparib:siRNAsi53BP1+siBRCA1                  0.9627    
## Olaparib:siRNAsiBRCA1                          0.0128 *  
## Olaparib:genotypeALC1KO                      6.47e-05 ***
## siRNAsi53BP1:genotypeALC1KO                    0.6177    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO            0.7475    
## siRNAsiBRCA1:genotypeALC1KO                    0.2743    
## Olaparib:siRNAsi53BP1:genotypeALC1KO           0.5530    
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO   0.7588    
## Olaparib:siRNAsiBRCA1:genotypeALC1KO           0.2871    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.107 on 112 degrees of freedom
## Multiple R-squared:  0.9007, Adjusted R-squared:  0.8875 
## F-statistic: 67.76 on 15 and 112 DF,  p-value: < 2.2e-16

cat("AIC: ", AIC(fit3))

## AIC:  -192.0674

simres <- simulateResiduals(fittedModel = fit3)
plot(simres)

fit4 <- lmer(Counts ~ Olaparib*siRNA*genotype + (1|UID), data = dataset)
print(summary(fit4))

## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Counts ~ Olaparib * siRNA * genotype + (1 | UID)
##    Data: dataset
## 
## REML criterion at convergence: 1622.4
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.9007 -0.5748 -0.0717  0.5734  2.2507 
## 
## Random effects:
##  Groups   Name        Variance Std.Dev.
##  UID      (Intercept) 197856   444.8   
##  Residual              38460   196.1   
## Number of obs: 128, groups:  UID, 32
## 
## Fixed effects:
##                                               Estimate Std. Error        df
## (Intercept)                                   2645.966    238.525    28.803
## Olaparib                                      -279.540     38.162    88.000
## siRNAsi53BP1                                    80.926    337.326    28.803
## siRNAsi53BP1+siBRCA1                          -662.557    337.326    28.803
## siRNAsiBRCA1                                 -1211.136    337.326    28.803
## genotypeALC1KO                                -938.475    337.326    28.803
## Olaparib:siRNAsi53BP1                          -64.955     53.969    88.000
## Olaparib:siRNAsi53BP1+siBRCA1                   84.874     53.969    88.000
## Olaparib:siRNAsiBRCA1                           13.698     53.969    88.000
## Olaparib:genotypeALC1KO                       -149.784     53.969    88.000
## siRNAsi53BP1:genotypeALC1KO                   -558.350    477.051    28.803
## siRNAsi53BP1+siBRCA1:genotypeALC1KO           -192.261    477.051    28.803
## siRNAsiBRCA1:genotypeALC1KO                      5.367    477.051    28.803
## Olaparib:siRNAsi53BP1:genotypeALC1KO           202.473     76.324    88.000
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO   119.029     76.324    88.000
## Olaparib:siRNAsiBRCA1:genotypeALC1KO           276.501     76.324    88.000
##                                              t value Pr(>|t|)    
## (Intercept)                                   11.093 6.50e-12 ***
## Olaparib                                      -7.325 1.08e-10 ***
## siRNAsi53BP1                                   0.240 0.812104    
## siRNAsi53BP1+siBRCA1                          -1.964 0.059229 .  
## siRNAsiBRCA1                                  -3.590 0.001209 ** 
## genotypeALC1KO                                -2.782 0.009428 ** 
## Olaparib:siRNAsi53BP1                         -1.204 0.231992    
## Olaparib:siRNAsi53BP1+siBRCA1                  1.573 0.119393    
## Olaparib:siRNAsiBRCA1                          0.254 0.800239    
## Olaparib:genotypeALC1KO                       -2.775 0.006735 ** 
## siRNAsi53BP1:genotypeALC1KO                   -1.170 0.251425    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO           -0.403 0.689909    
## siRNAsiBRCA1:genotypeALC1KO                    0.011 0.991101    
## Olaparib:siRNAsi53BP1:genotypeALC1KO           2.653 0.009470 ** 
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO   1.560 0.122465    
## Olaparib:siRNAsiBRCA1:genotypeALC1KO           3.623 0.000487 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

cat("AIC: ", AIC(fit4))

## AIC:  1658.358

simres <- simulateResiduals(fittedModel = fit4)
plot(simres)

Quadratic formula

fit5 <- lm(Counts ~ Experiment + poly(Olaparib,2)*siRNA*genotype, data = dataset)
print(summary(fit5))

## 
## Call:
## lm(formula = Counts ~ Experiment + poly(Olaparib, 2) * siRNA * 
##     genotype, data = dataset)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -653.69 -238.10    9.73  216.34  849.41 
## 
## Coefficients:
##                                                        Estimate Std. Error
## (Intercept)                                             1967.17     104.62
## Experimentexp2                                           445.94      89.22
## Experimentexp3                                           389.25      89.22
## Experimentexp4                                          -197.37      89.22
## poly(Olaparib, 2)1                                     -4063.13    1009.39
## poly(Olaparib, 2)2                                     -1834.91    1009.39
## siRNAsi53BP1                                             -39.75     126.17
## siRNAsi53BP1+siBRCA1                                    -504.87     126.17
## siRNAsiBRCA1                                           -1185.69     126.17
## genotypeALC1KO                                         -1216.75     126.17
## poly(Olaparib, 2)1:siRNAsi53BP1                         -944.12    1427.49
## poly(Olaparib, 2)2:siRNAsi53BP1                          302.40    1427.49
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                 1233.64    1427.49
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                 1565.84    1427.49
## poly(Olaparib, 2)1:siRNAsiBRCA1                          199.10    1427.49
## poly(Olaparib, 2)2:siRNAsiBRCA1                         2351.59    1427.49
## poly(Olaparib, 2)1:genotypeALC1KO                      -2177.12    1427.49
## poly(Olaparib, 2)2:genotypeALC1KO                       3444.07    1427.49
## siRNAsi53BP1:genotypeALC1KO                             -182.19     178.44
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                       28.87     178.44
## siRNAsiBRCA1:genotypeALC1KO                              519.06     178.44
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO          2942.95    2018.78
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO         -1295.71    2018.78
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  1730.08    2018.78
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -2295.16    2018.78
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO          4018.95    2018.78
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO         -3685.15    2018.78
##                                                        t value Pr(>|t|)    
## (Intercept)                                             18.803  < 2e-16 ***
## Experimentexp2                                           4.998 2.44e-06 ***
## Experimentexp3                                           4.363 3.10e-05 ***
## Experimentexp4                                          -2.212  0.02920 *  
## poly(Olaparib, 2)1                                      -4.025  0.00011 ***
## poly(Olaparib, 2)2                                      -1.818  0.07205 .  
## siRNAsi53BP1                                            -0.315  0.75338    
## siRNAsi53BP1+siBRCA1                                    -4.001  0.00012 ***
## siRNAsiBRCA1                                            -9.397 1.91e-15 ***
## genotypeALC1KO                                          -9.643 5.48e-16 ***
## poly(Olaparib, 2)1:siRNAsi53BP1                         -0.661  0.50987    
## poly(Olaparib, 2)2:siRNAsi53BP1                          0.212  0.83266    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                  0.864  0.38952    
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                  1.097  0.27529    
## poly(Olaparib, 2)1:siRNAsiBRCA1                          0.139  0.88936    
## poly(Olaparib, 2)2:siRNAsiBRCA1                          1.647  0.10259    
## poly(Olaparib, 2)1:genotypeALC1KO                       -1.525  0.13035    
## poly(Olaparib, 2)2:genotypeALC1KO                        2.413  0.01764 *  
## siRNAsi53BP1:genotypeALC1KO                             -1.021  0.30968    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                      0.162  0.87177    
## siRNAsiBRCA1:genotypeALC1KO                              2.909  0.00446 ** 
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO           1.458  0.14800    
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO          -0.642  0.52244    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO   0.857  0.39348    
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -1.137  0.25827    
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO           1.991  0.04921 *  
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO          -1.825  0.07089 .  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 356.9 on 101 degrees of freedom
## Multiple R-squared:  0.8708, Adjusted R-squared:  0.8375 
## F-statistic: 26.18 on 26 and 101 DF,  p-value: < 2.2e-16

cat("AIC: ", AIC(fit5))

## AIC:  1893.534

simres <- simulateResiduals(fittedModel = fit5)
plot(simres)

fit6 <- lm(NormCounts ~ poly(Olaparib,2)*siRNA*genotype, data = dataset)
print(summary(fit6))

## 
## Call:
## lm(formula = NormCounts ~ poly(Olaparib, 2) * siRNA * genotype, 
##     data = dataset)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -0.49865 -0.08137  0.00024  0.08742  0.54005 
## 
## Coefficients:
##                                                          Estimate Std. Error
## (Intercept)                                             1.000e+00  4.146e-02
## poly(Olaparib, 2)1                                     -1.973e+00  4.691e-01
## poly(Olaparib, 2)2                                     -8.808e-01  4.691e-01
## siRNAsi53BP1                                           -2.231e-16  5.864e-02
## siRNAsi53BP1+siBRCA1                                    1.601e-16  5.864e-02
## siRNAsiBRCA1                                            2.393e-17  5.864e-02
## genotypeALC1KO                                         -6.681e-16  5.864e-02
## poly(Olaparib, 2)1:siRNAsi53BP1                        -5.603e-01  6.634e-01
## poly(Olaparib, 2)2:siRNAsi53BP1                         1.255e-01  6.634e-01
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                -1.515e-01  6.634e-01
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                 8.736e-01  6.634e-01
## poly(Olaparib, 2)1:siRNAsiBRCA1                        -2.295e+00  6.634e-01
## poly(Olaparib, 2)2:siRNAsiBRCA1                         1.021e+00  6.634e-01
## poly(Olaparib, 2)1:genotypeALC1KO                      -5.126e+00  6.634e-01
## poly(Olaparib, 2)2:genotypeALC1KO                       2.709e+00  6.634e-01
## siRNAsi53BP1:genotypeALC1KO                             1.460e-16  8.292e-02
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                    -2.043e-16  8.292e-02
## siRNAsiBRCA1:genotypeALC1KO                            -4.197e-17  8.292e-02
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO          1.163e+00  9.382e-01
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO         -1.002e+00  9.382e-01
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.028e+00  9.382e-01
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.787e-01  9.382e-01
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO          1.182e+00  9.382e-01
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO         -1.788e+00  9.382e-01
##                                                        t value Pr(>|t|)    
## (Intercept)                                             24.119  < 2e-16 ***
## poly(Olaparib, 2)1                                      -4.205 5.54e-05 ***
## poly(Olaparib, 2)2                                      -1.878 0.063219 .  
## siRNAsi53BP1                                             0.000 1.000000    
## siRNAsi53BP1+siBRCA1                                     0.000 1.000000    
## siRNAsiBRCA1                                             0.000 1.000000    
## genotypeALC1KO                                           0.000 1.000000    
## poly(Olaparib, 2)1:siRNAsi53BP1                         -0.845 0.400241    
## poly(Olaparib, 2)2:siRNAsi53BP1                          0.189 0.850307    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                 -0.228 0.819750    
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                  1.317 0.190765    
## poly(Olaparib, 2)1:siRNAsiBRCA1                         -3.460 0.000786 ***
## poly(Olaparib, 2)2:siRNAsiBRCA1                          1.539 0.126825    
## poly(Olaparib, 2)1:genotypeALC1KO                       -7.726 7.25e-12 ***
## poly(Olaparib, 2)2:genotypeALC1KO                        4.083 8.75e-05 ***
## siRNAsi53BP1:genotypeALC1KO                              0.000 1.000000    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                      0.000 1.000000    
## siRNAsiBRCA1:genotypeALC1KO                              0.000 1.000000    
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO           1.240 0.217734    
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO          -1.068 0.288079    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -1.096 0.275776    
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.191 0.849282    
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO           1.260 0.210604    
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO          -1.906 0.059369 .  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.1658 on 104 degrees of freedom
## Multiple R-squared:  0.9231, Adjusted R-squared:  0.9061 
## F-statistic: 54.27 on 23 and 104 DF,  p-value: < 2.2e-16

cat("AIC: ", AIC(fit6))

## AIC:  -73.28383

simres <- simulateResiduals(fittedModel = fit6)
plot(simres)

fit7 <- lm(NormCounts2 ~ poly(Olaparib,2)*siRNA*genotype, data = dataset)
print(summary(fit7))

## 
## Call:
## lm(formula = NormCounts2 ~ poly(Olaparib, 2) * siRNA * genotype, 
##     data = dataset)
## 
## Residuals:
##       Min        1Q    Median        3Q       Max 
## -0.235066 -0.048533  0.000176  0.053866  0.242777 
## 
## Coefficients:
##                                                         Estimate Std. Error
## (Intercept)                                             0.841093   0.022641
## poly(Olaparib, 2)1                                     -1.659109   0.256151
## poly(Olaparib, 2)2                                     -0.740846   0.256151
## siRNAsi53BP1                                           -0.050843   0.032019
## siRNAsi53BP1+siBRCA1                                   -0.050571   0.032019
## siRNAsiBRCA1                                           -0.198613   0.032019
## genotypeALC1KO                                         -0.357112   0.032019
## poly(Olaparib, 2)1:siRNAsi53BP1                        -0.342512   0.362252
## poly(Olaparib, 2)2:siRNAsi53BP1                         0.143967   0.362252
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                -0.020047   0.362252
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                 0.735155   0.362252
## poly(Olaparib, 2)1:siRNAsiBRCA1                        -1.082742   0.362252
## poly(Olaparib, 2)2:siRNAsiBRCA1                         0.830908   0.362252
## poly(Olaparib, 2)1:genotypeALC1KO                      -1.776242   0.362252
## poly(Olaparib, 2)2:genotypeALC1KO                       1.625433   0.362252
## siRNAsi53BP1:genotypeALC1KO                             0.093085   0.045281
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                     0.006535   0.045281
## siRNAsiBRCA1:genotypeALC1KO                             0.186036   0.045281
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO          0.360026   0.512301
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO         -0.527875   0.512301
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.186264   0.512301
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.509928   0.512301
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO          0.647226   0.512301
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO         -1.215675   0.512301
##                                                        t value Pr(>|t|)    
## (Intercept)                                             37.150  < 2e-16 ***
## poly(Olaparib, 2)1                                      -6.477 3.16e-09 ***
## poly(Olaparib, 2)2                                      -2.892  0.00466 ** 
## siRNAsi53BP1                                            -1.588  0.11534    
## siRNAsi53BP1+siBRCA1                                    -1.579  0.11728    
## siRNAsiBRCA1                                            -6.203 1.14e-08 ***
## genotypeALC1KO                                         -11.153  < 2e-16 ***
## poly(Olaparib, 2)1:siRNAsi53BP1                         -0.946  0.34659    
## poly(Olaparib, 2)2:siRNAsi53BP1                          0.397  0.69187    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                 -0.055  0.95597    
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                  2.029  0.04497 *  
## poly(Olaparib, 2)1:siRNAsiBRCA1                         -2.989  0.00349 ** 
## poly(Olaparib, 2)2:siRNAsiBRCA1                          2.294  0.02382 *  
## poly(Olaparib, 2)1:genotypeALC1KO                       -4.903 3.49e-06 ***
## poly(Olaparib, 2)2:genotypeALC1KO                        4.487 1.87e-05 ***
## siRNAsi53BP1:genotypeALC1KO                              2.056  0.04232 *  
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                      0.144  0.88553    
## siRNAsiBRCA1:genotypeALC1KO                              4.108 7.96e-05 ***
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO           0.703  0.48377    
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO          -1.030  0.30521    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.364  0.71691    
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.995  0.32187    
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO           1.263  0.20928    
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO          -2.373  0.01948 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.09056 on 104 degrees of freedom
## Multiple R-squared:  0.9339, Adjusted R-squared:  0.9193 
## F-statistic: 63.92 on 23 and 104 DF,  p-value: < 2.2e-16

cat("AIC: ", AIC(fit7))

## AIC:  -228.1676

simres <- simulateResiduals(fittedModel = fit7)
plot(simres)

fit8 <- lmer(Counts ~ poly(Olaparib,2)*siRNA*genotype + (1|UID), data = dataset)
print(summary(fit8))

## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Counts ~ poly(Olaparib, 2) * siRNA * genotype + (1 | UID)
##    Data: dataset
## 
## REML criterion at convergence: 1427.1
## 
## Scaled residuals: 
##      Min       1Q   Median       3Q      Max 
## -2.52515 -0.47579 -0.02532  0.47074  2.39428 
## 
## Random effects:
##  Groups   Name        Variance Std.Dev.
##  UID      (Intercept) 200751   448.1   
##  Residual              26878   163.9   
## Number of obs: 128, groups:  UID, 32
## 
## Fixed effects:
##                                                        Estimate Std. Error
## (Intercept)                                             2126.62     227.74
## poly(Olaparib, 2)1                                     -4063.13     463.71
## poly(Olaparib, 2)2                                     -1834.91     463.71
## siRNAsi53BP1                                             -39.75     322.08
## siRNAsi53BP1+siBRCA1                                    -504.87     322.08
## siRNAsiBRCA1                                           -1185.69     322.08
## genotypeALC1KO                                         -1216.75     322.08
## poly(Olaparib, 2)1:siRNAsi53BP1                         -944.12     655.78
## poly(Olaparib, 2)2:siRNAsi53BP1                          302.40     655.78
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                 1233.64     655.78
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                 1565.84     655.78
## poly(Olaparib, 2)1:siRNAsiBRCA1                          199.10     655.78
## poly(Olaparib, 2)2:siRNAsiBRCA1                         2351.59     655.78
## poly(Olaparib, 2)1:genotypeALC1KO                      -2177.12     655.78
## poly(Olaparib, 2)2:genotypeALC1KO                       3444.07     655.78
## siRNAsi53BP1:genotypeALC1KO                             -182.19     455.49
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                       28.87     455.49
## siRNAsiBRCA1:genotypeALC1KO                              519.06     455.49
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO          2942.95     927.42
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO         -1295.71     927.42
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  1730.08     927.42
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -2295.16     927.42
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO          4018.95     927.42
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO         -3685.15     927.42
##                                                              df t value
## (Intercept)                                               24.00   9.338
## poly(Olaparib, 2)1                                        80.00  -8.762
## poly(Olaparib, 2)2                                        80.00  -3.957
## siRNAsi53BP1                                              24.00  -0.123
## siRNAsi53BP1+siBRCA1                                      24.00  -1.568
## siRNAsiBRCA1                                              24.00  -3.681
## genotypeALC1KO                                            24.00  -3.778
## poly(Olaparib, 2)1:siRNAsi53BP1                           80.00  -1.440
## poly(Olaparib, 2)2:siRNAsi53BP1                           80.00   0.461
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                   80.00   1.881
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                   80.00   2.388
## poly(Olaparib, 2)1:siRNAsiBRCA1                           80.00   0.304
## poly(Olaparib, 2)2:siRNAsiBRCA1                           80.00   3.586
## poly(Olaparib, 2)1:genotypeALC1KO                         80.00  -3.320
## poly(Olaparib, 2)2:genotypeALC1KO                         80.00   5.252
## siRNAsi53BP1:genotypeALC1KO                               24.00  -0.400
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                       24.00   0.063
## siRNAsiBRCA1:genotypeALC1KO                               24.00   1.140
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO            80.00   3.173
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO            80.00  -1.397
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO    80.00   1.865
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO    80.00  -2.475
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO            80.00   4.333
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO            80.00  -3.974
##                                                        Pr(>|t|)    
## (Intercept)                                            1.84e-09 ***
## poly(Olaparib, 2)1                                     2.58e-13 ***
## poly(Olaparib, 2)2                                     0.000163 ***
## siRNAsi53BP1                                           0.902805    
## siRNAsi53BP1+siBRCA1                                   0.130079    
## siRNAsiBRCA1                                           0.001174 ** 
## genotypeALC1KO                                         0.000922 ***
## poly(Olaparib, 2)1:siRNAsi53BP1                        0.153859    
## poly(Olaparib, 2)2:siRNAsi53BP1                        0.645960    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                0.063586 .  
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                0.019310 *  
## poly(Olaparib, 2)1:siRNAsiBRCA1                        0.762222    
## poly(Olaparib, 2)2:siRNAsiBRCA1                        0.000576 ***
## poly(Olaparib, 2)1:genotypeALC1KO                      0.001358 ** 
## poly(Olaparib, 2)2:genotypeALC1KO                      1.21e-06 ***
## siRNAsi53BP1:genotypeALC1KO                            0.692708    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                    0.949978    
## siRNAsiBRCA1:genotypeALC1KO                            0.265711    
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO         0.002139 ** 
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO         0.166242    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.065780 .  
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.015446 *  
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO         4.23e-05 ***
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO         0.000154 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

cat("AIC: ", AIC(fit8))

## AIC:  1479.072

simres <- simulateResiduals(fittedModel = fit8)
plot(simres)

Cubic formula

fit9 <- lm(Counts ~ Experiment + poly(Olaparib,3)*siRNA*genotype, data = dataset)
print(summary(fit9))

## 
## Call:
## lm(formula = Counts ~ Experiment + poly(Olaparib, 3) * siRNA * 
##     genotype, data = dataset)
## 
## Residuals:
##    Min     1Q Median     3Q    Max 
## -682.5 -229.8   16.2  210.0  844.8 
## 
## Coefficients:
##                                                        Estimate Std. Error
## (Intercept)                                             1967.17     108.46
## Experimentexp2                                           445.94      92.49
## Experimentexp3                                           389.25      92.49
## Experimentexp4                                          -197.37      92.49
## poly(Olaparib, 3)1                                     -4063.13    1046.45
## poly(Olaparib, 3)2                                     -1834.91    1046.45
## poly(Olaparib, 3)3                                      -658.33    1046.45
## siRNAsi53BP1                                             -39.75     130.81
## siRNAsi53BP1+siBRCA1                                    -504.87     130.81
## siRNAsiBRCA1                                           -1185.69     130.81
## genotypeALC1KO                                         -1216.75     130.81
## poly(Olaparib, 3)1:siRNAsi53BP1                         -944.12    1479.91
## poly(Olaparib, 3)2:siRNAsi53BP1                          302.40    1479.91
## poly(Olaparib, 3)3:siRNAsi53BP1                          486.10    1479.91
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                 1233.64    1479.91
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                 1565.84    1479.91
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                 1284.68    1479.91
## poly(Olaparib, 3)1:siRNAsiBRCA1                          199.10    1479.91
## poly(Olaparib, 3)2:siRNAsiBRCA1                         2351.59    1479.91
## poly(Olaparib, 3)3:siRNAsiBRCA1                          593.91    1479.91
## poly(Olaparib, 3)1:genotypeALC1KO                      -2177.12    1479.91
## poly(Olaparib, 3)2:genotypeALC1KO                       3444.07    1479.91
## poly(Olaparib, 3)3:genotypeALC1KO                        375.79    1479.91
## siRNAsi53BP1:genotypeALC1KO                             -182.19     184.99
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                       28.87     184.99
## siRNAsiBRCA1:genotypeALC1KO                              519.06     184.99
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO          2942.95    2092.91
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO         -1295.71    2092.91
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO            77.89    2092.91
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  1730.08    2092.91
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -2295.16    2092.91
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1183.92    2092.91
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO          4018.95    2092.91
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO         -3685.15    2092.91
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO          -196.83    2092.91
##                                                        t value Pr(>|t|)    
## (Intercept)                                             18.137  < 2e-16 ***
## Experimentexp2                                           4.821 5.55e-06 ***
## Experimentexp3                                           4.208 5.93e-05 ***
## Experimentexp4                                          -2.134 0.035481 *  
## poly(Olaparib, 3)1                                      -3.883 0.000193 ***
## poly(Olaparib, 3)2                                      -1.753 0.082819 .  
## poly(Olaparib, 3)3                                      -0.629 0.530825    
## siRNAsi53BP1                                            -0.304 0.761896    
## siRNAsi53BP1+siBRCA1                                    -3.860 0.000209 ***
## siRNAsiBRCA1                                            -9.064 1.95e-14 ***
## genotypeALC1KO                                          -9.302 6.14e-15 ***
## poly(Olaparib, 3)1:siRNAsi53BP1                         -0.638 0.525069    
## poly(Olaparib, 3)2:siRNAsi53BP1                          0.204 0.838538    
## poly(Olaparib, 3)3:siRNAsi53BP1                          0.328 0.743300    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                  0.834 0.406646    
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                  1.058 0.292766    
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                  0.868 0.387587    
## poly(Olaparib, 3)1:siRNAsiBRCA1                          0.135 0.893273    
## poly(Olaparib, 3)2:siRNAsiBRCA1                          1.589 0.115452    
## poly(Olaparib, 3)3:siRNAsiBRCA1                          0.401 0.689108    
## poly(Olaparib, 3)1:genotypeALC1KO                       -1.471 0.144636    
## poly(Olaparib, 3)2:genotypeALC1KO                        2.327 0.022124 *  
## poly(Olaparib, 3)3:genotypeALC1KO                        0.254 0.800114    
## siRNAsi53BP1:genotypeALC1KO                             -0.985 0.327250    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                      0.156 0.876300    
## siRNAsiBRCA1:genotypeALC1KO                              2.806 0.006111 ** 
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO           1.406 0.163011    
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO          -0.619 0.537367    
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO           0.037 0.970393    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO   0.827 0.410557    
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -1.097 0.275632    
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.566 0.572973    
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO           1.920 0.057888 .  
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO          -1.761 0.081563 .  
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO          -0.094 0.925276    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 370 on 93 degrees of freedom
## Multiple R-squared:  0.8721, Adjusted R-squared:  0.8254 
## F-statistic: 18.66 on 34 and 93 DF,  p-value: < 2.2e-16

cat("AIC: ", AIC(fit9))

## AIC:  1908.202

simres <- simulateResiduals(fittedModel = fit9)
plot(simres)

fit10 <- lm(NormCounts ~ poly(Olaparib,3)*siRNA*genotype, data = dataset)
print(summary(fit10))

## 
## Call:
## lm(formula = NormCounts ~ poly(Olaparib, 3) * siRNA * genotype, 
##     data = dataset)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -0.48516 -0.08021  0.00374  0.08583  0.52791 
## 
## Coefficients:
##                                                          Estimate Std. Error
## (Intercept)                                             1.000e+00  4.223e-02
## poly(Olaparib, 3)1                                     -1.973e+00  4.778e-01
## poly(Olaparib, 3)2                                     -8.808e-01  4.778e-01
## poly(Olaparib, 3)3                                     -3.028e-01  4.778e-01
## siRNAsi53BP1                                            8.493e-17  5.973e-02
## siRNAsi53BP1+siBRCA1                                    3.307e-16  5.973e-02
## siRNAsiBRCA1                                           -6.790e-17  5.973e-02
## genotypeALC1KO                                         -5.075e-16  5.973e-02
## poly(Olaparib, 3)1:siRNAsi53BP1                        -5.603e-01  6.757e-01
## poly(Olaparib, 3)2:siRNAsi53BP1                         1.255e-01  6.757e-01
## poly(Olaparib, 3)3:siRNAsi53BP1                         2.073e-01  6.757e-01
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                -1.515e-01  6.757e-01
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                 8.736e-01  6.757e-01
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                 5.385e-01  6.757e-01
## poly(Olaparib, 3)1:siRNAsiBRCA1                        -2.295e+00  6.757e-01
## poly(Olaparib, 3)2:siRNAsiBRCA1                         1.021e+00  6.757e-01
## poly(Olaparib, 3)3:siRNAsiBRCA1                         3.140e-01  6.757e-01
## poly(Olaparib, 3)1:genotypeALC1KO                      -5.126e+00  6.757e-01
## poly(Olaparib, 3)2:genotypeALC1KO                       2.709e+00  6.757e-01
## poly(Olaparib, 3)3:genotypeALC1KO                      -1.721e-01  6.757e-01
## siRNAsi53BP1:genotypeALC1KO                            -3.885e-17  8.447e-02
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                    -4.261e-16  8.447e-02
## siRNAsiBRCA1:genotypeALC1KO                            -1.683e-16  8.447e-02
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO          1.163e+00  9.557e-01
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO         -1.002e+00  9.557e-01
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO          5.200e-01  9.557e-01
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.028e+00  9.557e-01
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.787e-01  9.557e-01
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -5.458e-01  9.557e-01
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO          1.182e+00  9.557e-01
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO         -1.788e+00  9.557e-01
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO          6.968e-01  9.557e-01
##                                                        t value Pr(>|t|)    
## (Intercept)                                             23.677  < 2e-16 ***
## poly(Olaparib, 3)1                                      -4.128 7.80e-05 ***
## poly(Olaparib, 3)2                                      -1.843 0.068359 .  
## poly(Olaparib, 3)3                                      -0.634 0.527770    
## siRNAsi53BP1                                             0.000 1.000000    
## siRNAsi53BP1+siBRCA1                                     0.000 1.000000    
## siRNAsiBRCA1                                             0.000 1.000000    
## genotypeALC1KO                                           0.000 1.000000    
## poly(Olaparib, 3)1:siRNAsi53BP1                         -0.829 0.409047    
## poly(Olaparib, 3)2:siRNAsi53BP1                          0.186 0.853045    
## poly(Olaparib, 3)3:siRNAsi53BP1                          0.307 0.759698    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                 -0.224 0.823029    
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                  1.293 0.199180    
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                  0.797 0.427501    
## poly(Olaparib, 3)1:siRNAsiBRCA1                         -3.396 0.000995 ***
## poly(Olaparib, 3)2:siRNAsiBRCA1                          1.511 0.134098    
## poly(Olaparib, 3)3:siRNAsiBRCA1                          0.465 0.643245    
## poly(Olaparib, 3)1:genotypeALC1KO                       -7.585 2.12e-11 ***
## poly(Olaparib, 3)2:genotypeALC1KO                        4.008 0.000121 ***
## poly(Olaparib, 3)3:genotypeALC1KO                       -0.255 0.799459    
## siRNAsi53BP1:genotypeALC1KO                              0.000 1.000000    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                      0.000 1.000000    
## siRNAsiBRCA1:genotypeALC1KO                              0.000 1.000000    
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO           1.217 0.226438    
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO          -1.048 0.297146    
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO           0.544 0.587587    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -1.076 0.284814    
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.187 0.852038    
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.571 0.569225    
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO           1.237 0.219241    
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO          -1.871 0.064330 .  
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO           0.729 0.467676    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.1689 on 96 degrees of freedom
## Multiple R-squared:  0.9263, Adjusted R-squared:  0.9025 
## F-statistic: 38.94 on 31 and 96 DF,  p-value: < 2.2e-16

cat("AIC: ", AIC(fit10))

## AIC:  -62.8016

simres <- simulateResiduals(fittedModel = fit10)
plot(simres)

fit11 <- lm(NormCounts2 ~ poly(Olaparib,3)*siRNA*genotype, data = dataset)
print(summary(fit11))

## 
## Call:
## lm(formula = NormCounts2 ~ poly(Olaparib, 3) * siRNA * genotype, 
##     data = dataset)
## 
## Residuals:
##       Min        1Q    Median        3Q       Max 
## -0.228704 -0.042322  0.002445  0.054386  0.232250 
## 
## Coefficients:
##                                                         Estimate Std. Error
## (Intercept)                                             0.841093   0.023068
## poly(Olaparib, 3)1                                     -1.659109   0.260990
## poly(Olaparib, 3)2                                     -0.740846   0.260990
## poly(Olaparib, 3)3                                     -0.254690   0.260990
## siRNAsi53BP1                                           -0.050843   0.032624
## siRNAsi53BP1+siBRCA1                                   -0.050571   0.032624
## siRNAsiBRCA1                                           -0.198613   0.032624
## genotypeALC1KO                                         -0.357112   0.032624
## poly(Olaparib, 3)1:siRNAsi53BP1                        -0.342512   0.369096
## poly(Olaparib, 3)2:siRNAsi53BP1                         0.143967   0.369096
## poly(Olaparib, 3)3:siRNAsi53BP1                         0.179203   0.369096
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                -0.020047   0.369096
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                 0.735155   0.369096
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                 0.440989   0.369096
## poly(Olaparib, 3)1:siRNAsiBRCA1                        -1.082742   0.369096
## poly(Olaparib, 3)2:siRNAsiBRCA1                         0.830908   0.369096
## poly(Olaparib, 3)3:siRNAsiBRCA1                         0.261866   0.369096
## poly(Olaparib, 3)1:genotypeALC1KO                      -1.776242   0.369096
## poly(Olaparib, 3)2:genotypeALC1KO                       1.625433   0.369096
## poly(Olaparib, 3)3:genotypeALC1KO                       0.024820   0.369096
## siRNAsi53BP1:genotypeALC1KO                             0.093085   0.046137
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                     0.006535   0.046137
## siRNAsiBRCA1:genotypeALC1KO                             0.186036   0.046137
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO          0.360026   0.521980
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO         -0.527875   0.521980
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO          0.183467   0.521980
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.186264   0.521980
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.509928   0.521980
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.423311   0.521980
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO          0.647226   0.521980
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO         -1.215675   0.521980
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO          0.220606   0.521980
##                                                        t value Pr(>|t|)    
## (Intercept)                                             36.461  < 2e-16 ***
## poly(Olaparib, 3)1                                      -6.357 6.92e-09 ***
## poly(Olaparib, 3)2                                      -2.839 0.005530 ** 
## poly(Olaparib, 3)3                                      -0.976 0.331586    
## siRNAsi53BP1                                            -1.558 0.122415    
## siRNAsi53BP1+siBRCA1                                    -1.550 0.124404    
## siRNAsiBRCA1                                            -6.088 2.35e-08 ***
## genotypeALC1KO                                         -10.946  < 2e-16 ***
## poly(Olaparib, 3)1:siRNAsi53BP1                         -0.928 0.355747    
## poly(Olaparib, 3)2:siRNAsi53BP1                          0.390 0.697361    
## poly(Olaparib, 3)3:siRNAsi53BP1                          0.486 0.628414    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                 -0.054 0.956799    
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                  1.992 0.049237 *  
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                  1.195 0.235116    
## poly(Olaparib, 3)1:siRNAsiBRCA1                         -2.933 0.004192 ** 
## poly(Olaparib, 3)2:siRNAsiBRCA1                          2.251 0.026654 *  
## poly(Olaparib, 3)3:siRNAsiBRCA1                          0.709 0.479747    
## poly(Olaparib, 3)1:genotypeALC1KO                       -4.812 5.54e-06 ***
## poly(Olaparib, 3)2:genotypeALC1KO                        4.404 2.76e-05 ***
## poly(Olaparib, 3)3:genotypeALC1KO                        0.067 0.946526    
## siRNAsi53BP1:genotypeALC1KO                              2.018 0.046427 *  
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                      0.142 0.887657    
## siRNAsiBRCA1:genotypeALC1KO                              4.032 0.000111 ***
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO           0.690 0.492028    
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO          -1.011 0.314418    
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO           0.351 0.725996    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.357 0.721994    
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.977 0.331069    
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.811 0.419389    
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO           1.240 0.218019    
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO          -2.329 0.021958 *  
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO           0.423 0.673509    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.09227 on 96 degrees of freedom
## Multiple R-squared:  0.9367, Adjusted R-squared:  0.9162 
## F-statistic: 45.82 on 31 and 96 DF,  p-value: < 2.2e-16

cat("AIC: ", AIC(fit11))

## AIC:  -217.6213

simres <- simulateResiduals(fittedModel = fit11)
plot(simres)

fit12 <- lmer(Counts ~ poly(Olaparib,3)*siRNA*genotype + (1|UID), data = dataset)
print(summary(fit12))

## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Counts ~ poly(Olaparib, 3) * siRNA * genotype + (1 | UID)
##    Data: dataset
## 
## REML criterion at convergence: 1309.1
## 
## Scaled residuals: 
##      Min       1Q   Median       3Q      Max 
## -2.43519 -0.42342  0.02777  0.45257  2.33975 
## 
## Random effects:
##  Groups   Name        Variance Std.Dev.
##  UID      (Intercept) 200467   447.7   
##  Residual              28016   167.4   
## Number of obs: 128, groups:  UID, 32
## 
## Fixed effects:
##                                                        Estimate Std. Error
## (Intercept)                                             2126.62     227.74
## poly(Olaparib, 3)1                                     -4063.13     473.42
## poly(Olaparib, 3)2                                     -1834.91     473.42
## poly(Olaparib, 3)3                                      -658.33     473.42
## siRNAsi53BP1                                             -39.75     322.08
## siRNAsi53BP1+siBRCA1                                    -504.87     322.08
## siRNAsiBRCA1                                           -1185.69     322.08
## genotypeALC1KO                                         -1216.75     322.08
## poly(Olaparib, 3)1:siRNAsi53BP1                         -944.12     669.52
## poly(Olaparib, 3)2:siRNAsi53BP1                          302.40     669.52
## poly(Olaparib, 3)3:siRNAsi53BP1                          486.10     669.52
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                 1233.64     669.52
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                 1565.84     669.52
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                 1284.68     669.52
## poly(Olaparib, 3)1:siRNAsiBRCA1                          199.10     669.52
## poly(Olaparib, 3)2:siRNAsiBRCA1                         2351.59     669.52
## poly(Olaparib, 3)3:siRNAsiBRCA1                          593.91     669.52
## poly(Olaparib, 3)1:genotypeALC1KO                      -2177.12     669.52
## poly(Olaparib, 3)2:genotypeALC1KO                       3444.07     669.52
## poly(Olaparib, 3)3:genotypeALC1KO                        375.79     669.52
## siRNAsi53BP1:genotypeALC1KO                             -182.19     455.49
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                       28.87     455.49
## siRNAsiBRCA1:genotypeALC1KO                              519.06     455.49
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO          2942.95     946.85
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO         -1295.71     946.85
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO            77.89     946.85
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  1730.08     946.85
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -2295.16     946.85
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1183.92     946.85
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO          4018.95     946.85
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO         -3685.15     946.85
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO          -196.83     946.85
##                                                              df t value
## (Intercept)                                               24.00   9.338
## poly(Olaparib, 3)1                                        72.00  -8.582
## poly(Olaparib, 3)2                                        72.00  -3.876
## poly(Olaparib, 3)3                                        72.00  -1.391
## siRNAsi53BP1                                              24.00  -0.123
## siRNAsi53BP1+siBRCA1                                      24.00  -1.568
## siRNAsiBRCA1                                              24.00  -3.681
## genotypeALC1KO                                            24.00  -3.778
## poly(Olaparib, 3)1:siRNAsi53BP1                           72.00  -1.410
## poly(Olaparib, 3)2:siRNAsi53BP1                           72.00   0.452
## poly(Olaparib, 3)3:siRNAsi53BP1                           72.00   0.726
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                   72.00   1.843
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                   72.00   2.339
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                   72.00   1.919
## poly(Olaparib, 3)1:siRNAsiBRCA1                           72.00   0.297
## poly(Olaparib, 3)2:siRNAsiBRCA1                           72.00   3.512
## poly(Olaparib, 3)3:siRNAsiBRCA1                           72.00   0.887
## poly(Olaparib, 3)1:genotypeALC1KO                         72.00  -3.252
## poly(Olaparib, 3)2:genotypeALC1KO                         72.00   5.144
## poly(Olaparib, 3)3:genotypeALC1KO                         72.00   0.561
## siRNAsi53BP1:genotypeALC1KO                               24.00  -0.400
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                       24.00   0.063
## siRNAsiBRCA1:genotypeALC1KO                               24.00   1.140
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO            72.00   3.108
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO            72.00  -1.368
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO            72.00   0.082
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO    72.00   1.827
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO    72.00  -2.424
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO    72.00  -1.250
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO            72.00   4.245
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO            72.00  -3.892
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO            72.00  -0.208
##                                                        Pr(>|t|)    
## (Intercept)                                            1.84e-09 ***
## poly(Olaparib, 3)1                                     1.25e-12 ***
## poly(Olaparib, 3)2                                     0.000232 ***
## poly(Olaparib, 3)3                                     0.168641    
## siRNAsi53BP1                                           0.902805    
## siRNAsi53BP1+siBRCA1                                   0.130079    
## siRNAsiBRCA1                                           0.001174 ** 
## genotypeALC1KO                                         0.000922 ***
## poly(Olaparib, 3)1:siRNAsi53BP1                        0.162804    
## poly(Olaparib, 3)2:siRNAsi53BP1                        0.652870    
## poly(Olaparib, 3)3:siRNAsi53BP1                        0.470172    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                0.069508 .  
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                0.022128 *  
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                0.058975 .  
## poly(Olaparib, 3)1:siRNAsiBRCA1                        0.767041    
## poly(Olaparib, 3)2:siRNAsiBRCA1                        0.000771 ***
## poly(Olaparib, 3)3:siRNAsiBRCA1                        0.377997    
## poly(Olaparib, 3)1:genotypeALC1KO                      0.001747 ** 
## poly(Olaparib, 3)2:genotypeALC1KO                      2.23e-06 ***
## poly(Olaparib, 3)3:genotypeALC1KO                      0.576353    
## siRNAsi53BP1:genotypeALC1KO                            0.692708    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                    0.949978    
## siRNAsiBRCA1:genotypeALC1KO                            0.265711    
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO         0.002695 ** 
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO         0.175428    
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO         0.934667    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.071813 .  
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.017864 *  
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.215209    
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO         6.43e-05 ***
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO         0.000220 ***
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO         0.835913    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

cat("AIC: ", AIC(fit12))

## AIC:  1377.126

simres <- simulateResiduals(fittedModel = fit12)
plot(simres)

Compare Results

ICtab(fit1,fit2,fit3,fit4,
      fit5,fit6,fit7,fit8,
      fit9,fit10,fit11,fit12,
      base=T)

##       AIC    dAIC   df
## fit7  -228.2    0.0 25
## fit11 -217.6   10.5 33
## fit3  -192.1   36.1 17
## fit6   -73.3  154.9 25
## fit10  -62.8  165.4 33
## fit2   -31.3  196.8 17
## fit12 1377.1 1605.3 34
## fit8  1479.1 1707.2 26
## fit4  1658.4 1886.5 18
## fit1  1889.3 2117.4 20
## fit5  1893.5 2121.7 28
## fit9  1908.2 2136.4 36

Final Result

fit <- fit7

output <- coef(summary(fit))
output <- output[grep("Olaparib", rownames(output)),]

rownames(output) <- gsub("poly\\(|, [1-3]\\)","", rownames(output) )
rownames(output) <- gsub("genotype",  paste0(" ",levels(dataset$genotype)[1], " vs. "), rownames(output))
rownames(output)[!(grepl("vs", rownames(output)))] <- paste(rownames(output)[!(grepl("vs", rownames(output)))], levels(dataset$genotype)[1],  sep = " in " )

rownames(output) <- gsub("siRNA",  paste0(" ",levels(dataset$siRNA)[1], " vs. "), rownames(output))
rownames(output)[!(grepl("vs.*vs|in", rownames(output)))] <- paste(rownames(output)[!(grepl("vs.*vs|in", rownames(output)))], levels(dataset$siRNA)[1],  sep = " in " )

rownames(output)[!(grepl("vs", rownames(output)))] <- paste(rownames(output)[!(grepl("vs", rownames(output)))], levels(dataset$siRNA)[1],  sep = " " )

# suggested result table
kable(output, row.names = T)

	Estimate	Std. Error	t value	Pr(>|t|)
Olaparib1 in WT siCtrl	-1.6591091	0.2561505	-6.4770871	0.0000000
Olaparib2 in WT siCtrl	-0.7408465	0.2561505	-2.8922312	0.0046590
Olaparib1: siCtrl vs. si53BP1 in WT	-0.3425124	0.3622515	-0.9455099	0.3465902
Olaparib2: siCtrl vs. si53BP1 in WT	0.1439674	0.3622515	0.3974238	0.6918695
Olaparib1: siCtrl vs. si53BP1+siBRCA1 in WT	-0.0200466	0.3622515	-0.0553389	0.9559746
Olaparib2: siCtrl vs. si53BP1+siBRCA1 in WT	0.7351549	0.3622515	2.0294045	0.0449712
Olaparib1: siCtrl vs. siBRCA1 in WT	-1.0827417	0.3622515	-2.9889225	0.0034938
Olaparib2: siCtrl vs. siBRCA1 in WT	0.8309079	0.3622515	2.2937320	0.0238166
Olaparib1: WT vs. ALC1KO in siCtrl	-1.7762418	0.3622515	-4.9033385	0.0000035
Olaparib2: WT vs. ALC1KO in siCtrl	1.6254326	0.3622515	4.4870277	0.0000187
Olaparib1: siCtrl vs. si53BP1: WT vs. ALC1KO	0.3600258	0.5123010	0.7027623	0.4837740
Olaparib2: siCtrl vs. si53BP1: WT vs. ALC1KO	-0.5278751	0.5123010	-1.0304002	0.3052125
Olaparib1: siCtrl vs. si53BP1+siBRCA1: WT vs. ALC1KO	-0.1862640	0.5123010	-0.3635831	0.7169074
Olaparib2: siCtrl vs. si53BP1+siBRCA1: WT vs. ALC1KO	-0.5099282	0.5123010	-0.9953684	0.3218674
Olaparib1: siCtrl vs. siBRCA1: WT vs. ALC1KO	0.6472261	0.5123010	1.2633708	0.2092808
Olaparib2: siCtrl vs. siBRCA1: WT vs. ALC1KO	-1.2156753	0.5123010	-2.3729707	0.0194828

write.table(output, file = "Figure5A_Stats_Ref_WT.txt", quote = F, sep = "\t", row.names = T, col.names = NA)

# re-fit with ALC1KO reference
dataset$genotype <- relevel(dataset$genotype, ref = "ALC1KO")
 
fit <- lm(NormCounts2 ~ poly(Olaparib,2)*siRNA*genotype, data = dataset)

output <- coef(summary(fit))
output <- output[grep("Olaparib", rownames(output)),]

rownames(output) <- gsub("poly\\(|, [1-3]\\)","", rownames(output) )
rownames(output) <- gsub("genotype",  paste0(" ",levels(dataset$genotype)[1], " vs. "), rownames(output))
rownames(output)[!(grepl("vs", rownames(output)))] <- paste(rownames(output)[!(grepl("vs", rownames(output)))], levels(dataset$genotype)[1],  sep = " in " )

rownames(output) <- gsub("siRNA",  paste0(" ",levels(dataset$siRNA)[1], " vs. "), rownames(output))
rownames(output)[!(grepl("vs.*vs|in", rownames(output)))] <- paste(rownames(output)[!(grepl("vs.*vs|in", rownames(output)))], levels(dataset$siRNA)[1],  sep = " in " )

rownames(output)[!(grepl("vs", rownames(output)))] <- paste(rownames(output)[!(grepl("vs", rownames(output)))], levels(dataset$siRNA)[1],  sep = " " )


# suggested result table
kable(output, row.names = T)

	Estimate	Std. Error	t value	Pr(>|t|)
Olaparib1 in ALC1KO siCtrl	-3.4353509	0.2561505	-13.4114549	0.0000000
Olaparib2 in ALC1KO siCtrl	0.8845861	0.2561505	3.4533843	0.0008020
Olaparib1: siCtrl vs. si53BP1 in ALC1KO	0.0175134	0.3622515	0.0483460	0.9615332
Olaparib2: siCtrl vs. si53BP1 in ALC1KO	-0.3839077	0.3622515	-1.0597822	0.2916988
Olaparib1: siCtrl vs. si53BP1+siBRCA1 in ALC1KO	-0.2063106	0.3622515	-0.5695231	0.5702293
Olaparib2: siCtrl vs. si53BP1+siBRCA1 in ALC1KO	0.2252266	0.3622515	0.6217411	0.5354727
Olaparib1: siCtrl vs. siBRCA1 in ALC1KO	-0.4355156	0.3622515	-1.2022465	0.2319983
Olaparib2: siCtrl vs. siBRCA1 in ALC1KO	-0.3847674	0.3622515	-1.0621553	0.2906254
Olaparib1: ALC1KO vs. WT in siCtrl	1.7762418	0.3622515	4.9033385	0.0000035
Olaparib2: ALC1KO vs. WT in siCtrl	-1.6254326	0.3622515	-4.4870277	0.0000187
Olaparib1: siCtrl vs. si53BP1: ALC1KO vs. WT	-0.3600258	0.5123010	-0.7027623	0.4837740
Olaparib2: siCtrl vs. si53BP1: ALC1KO vs. WT	0.5278751	0.5123010	1.0304002	0.3052125
Olaparib1: siCtrl vs. si53BP1+siBRCA1: ALC1KO vs. WT	0.1862640	0.5123010	0.3635831	0.7169074
Olaparib2: siCtrl vs. si53BP1+siBRCA1: ALC1KO vs. WT	0.5099282	0.5123010	0.9953684	0.3218674
Olaparib1: siCtrl vs. siBRCA1: ALC1KO vs. WT	-0.6472261	0.5123010	-1.2633708	0.2092808
Olaparib2: siCtrl vs. siBRCA1: ALC1KO vs. WT	1.2156753	0.5123010	2.3729707	0.0194828

write.table(output, file = "Figure5A_Stats_Ref_ALC1.txt", quote = F, sep = "\t", row.names = T, col.names = NA)

Anova

fit7a <- lm(NormCounts2 ~ poly(Olaparib,2)*siRNA*genotype, data = dataset)
fit7b <- lm(NormCounts2 ~ poly(Olaparib,2)*siRNA+genotype, data = dataset)

# anova table
anova(fit7a, fit7b)

## Analysis of Variance Table
## 
## Model 1: NormCounts2 ~ poly(Olaparib, 2) * siRNA * genotype
## Model 2: NormCounts2 ~ poly(Olaparib, 2) * siRNA + genotype
##   Res.Df     RSS  Df Sum of Sq      F  Pr(>F)    
## 1    104 0.85297                                 
## 2    115 2.00791 -11   -1.1549 12.802 5.2e-15 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1